5V will work, and so will 12V. The one consideration that comes to mind is that the 5V is limited in current by what the voltage regulator can supply... but you're not going to be near that limit with the number of LEDs you're planning... (I think that limit is ~1 A without a heatsink? But don't quote me )

When I put my specs into the LED calculator, it put the resistors after the LED (negative). I've heard of this method before, but I don't understand how it works. Can someone explain that to me? If I wanted to I could put it in between the 5 volts and the leds, right?